#!/bin/sh

# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`

# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

# function to test the exit status of a job
. ../check_failure.sh

$ECHO
$ECHO "$EXAMPLE_DIR : starting MD"
$ECHO

# set the needed environment variables
. ../environment_variables

# required executables and pseudopotentials
BIN_LIST="pw.x dos.x projwfc.x kvecs_FS.x bands_FS.x"
PSEUDO_LIST="Al.pbe-rrkj.UPF"

$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$ECHO "  checking that needed directories and files exist...\c"

# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
    if test ! -d $DIR ; then
        $ECHO
        $ECHO "ERROR: $DIR not existent or not a directory"
        $ECHO "Aborting"
        exit 1
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
cd $EXAMPLE_DIR/results

# check for executables
for FILE in $BIN_LIST ; do
    if test ! -x $BIN_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
        $ECHO "Aborting"
        exit 1
    fi
done
 
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
    if test ! -r $PSEUDO_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
        $ECHO "Aborting"
        exit 1
    fi
done
$ECHO " done"

# how to run executables
PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"
KUBO_COMMAND="$PARA_PREFIX $BIN_DIR/kubo.x $PARA_POSTFIX"
DOS_COMMAND="$PARA_PREFIX $BIN_DIR/dos.x $PARA_POSTFIX"
PROJWFC_COMMAND="$PARA_PREFIX $BIN_DIR/projwfc.x $PARA_POSTFIX"
KVECS_COMMAND="$BIN_DIR/kvecs_FS.x "
BANDS_COMMAND="$BIN_DIR/bands_FS.x "
$ECHO
$ECHO "  running pw.x as:      $PW_COMMAND"
$ECHO "  running dos.x as:     $DOS_COMMAND"
$ECHO "  running projwfc.x as: $PROJWFC_COMMAND"
$ECHO "  running kvecs_FS.x as:  $KVECS_COMMAND"
$ECHO "  running bands_FS.x as:  $BANDS_COMMAND"
$ECHO
 
# clean TMP_DIR
$ECHO "  cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/*
$ECHO " done"

# time step for molecular dynamics is in Rydberg atomic units 1 a.u.=4.8378 * 10^-17 s
# phys rev b 38 2 methfessel states fundamental freq of Si is ~42.25 Thz
# 1/10 of fundamental is about 50.0 a.u. then

# celldm at 293.2K is 4.0488 A = 7.6511 Bohr
# expansion at 14K is -0.419 % -> 7.683 Bohr
# expansion at 500K is +0.514 % -> 7.690 Bohr
# expansion at 800K is +1.408 % -> 7.759 Bohr

# dT taken from a simulation of liquid aluminium by alemay et. al. It is a
# dft based study and the time step they use is 6 fs.
# dt for MD of liquid Al of 6 fs so 1.5 fs for the solid should be
# ok. In pw.x units we have

# 1 a. u. = 4.8378 x 10^-17 s
#       = 4.8378 x 10^-2 fs

# so the time step is
# dt = 1.5 / 4.8378 x 10^-2 a.u.
#    = 31.0058291 a.u.

# 100 steps with nraise=1, restart file will use nraise=10

cat > md_Al_32.in << EOF
 &control
   calculation='md',
   restart_mode='from_scratch',
   pseudo_dir = '$PSEUDO_DIR',
   dt=7,
   nstep = 5000 ,
   outdir='./',
   prefix='Al32',
   disk_io ='low'
/
 &system
    ibrav = 1,
    celldm(1) = 15.518, 
    nat=  32, ntyp= 1, ecutwfc =50.0
    occupations =  'smearing',
    degauss = 0.0689386592,
    smearing = 'fd'
    nosym = .true.
/
 &electrons
    electron_maxstep = 999 ,
    conv_thr = 1.0e-6 ,
    mixing_beta = 0.7 ,
    startingwfc = 'atomic+random' ,
/
 &ions
    wfc_extrapolation = 'second_order',
    ion_temperature = 'rescale-v' ,
    tempw = 800.0 ,
    nraise = 20 ,
/
ATOMIC_SPECIES
 Al  26.98 Al.pbe-rrkj.UPF
ATOMIC_POSITIONS crystal
 Al  0.000000  0.000000  0.000000
 Al  0.250000  0.000000  0.250000
 Al  0.250000  0.250000  0.000000
 Al  0.000000  0.250000  0.250000
 Al  0.000000  0.000000  0.500000
 Al  0.250000  0.000000  0.750000
 Al  0.250000  0.250000  0.500000
 Al  0.000000  0.250000  0.750000
 Al  0.000000  0.500000  0.000000
 Al  0.250000  0.500000  0.250000
 Al  0.250000  0.750000  0.000000
 Al  0.000000  0.750000  0.250000
 Al  0.000000  0.500000  0.500000
 Al  0.250000  0.500000  0.750000
 Al  0.250000  0.750000  0.500000
 Al  0.000000  0.750000  0.750000
 Al  0.500000  0.000000  0.000000
 Al  0.750000  0.000000  0.250000
 Al  0.750000  0.250000  0.000000
 Al  0.500000  0.250000  0.250000
 Al  0.500000  0.000000  0.500000
 Al  0.750000  0.000000  0.750000
 Al  0.750000  0.250000  0.500000
 Al  0.500000  0.250000  0.750000
 Al  0.500000  0.500000  0.000000
 Al  0.750000  0.500000  0.250000
 Al  0.750000  0.750000  0.000000
 Al  0.500000  0.750000  0.250000
 Al  0.500000  0.500000  0.500000
 Al  0.750000  0.500000  0.750000
 Al  0.750000  0.750000  0.500000
 Al  0.500000  0.750000  0.750000
K_POINTS (automatic)
  1 1 1 0 0 0
EOF

$ECHO "  running the MD calculation for Al...\c"
mpiexec -n 8 $PW_COMMAND -ntg 4  < md_Al_32.in > md_Al32.out
#env OMP_NUM_THREADS=4 $PW_COMMAND  < md_Al_32.in > md_Al32.out
check_failure $?
$ECHO " done"

